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MarcHarford avatar MarcHarford commented on August 18, 2024 1

You´ve been amazing thank you!

from marrowquant.

MarcHarford avatar MarcHarford commented on August 18, 2024

Hiya Emily,

I´m currently using the same software and it is a fantastic however I wonder if you had any issue with the colour deconvolition section of the script? More specifically that trying to import it but it cannot be found even when specifying the directory?

Many thanks,
Marc

from marrowquant.

EST09 avatar EST09 commented on August 18, 2024

Hi,

I don't remember having that issue - but I was only interested in adipocytes so that's probably why?

For adipocytes I used: https://github.com/Naveiras-Lab/MarrowQuant2.0/tree/main and the stardust on adipocyte section
with qupath version 0.5.0 (on a mac).

Sorry I don't think this is super helpful to your question.

It's a fantastic tool for adipocytes though - thanks!

Best wishes,
Emily

from marrowquant.

MarcHarford avatar MarcHarford commented on August 18, 2024

Hiya,

Thank you so much for a quick response. All help is great help!. I too am only interested in adipocytes both within the bone marrow and also from WAT sections yet I run into the deconvoluation error in addition to the error you posted previously.

Many thanks for your time and help.

Best regards,
Marc

from marrowquant.

EST09 avatar EST09 commented on August 18, 2024

Hm - I remember this section in the readme being a little finicky (Setting up QuPath 0.3.1 for MarrowQuant) esp point 7 in https://github.com/Naveiras-Lab/MarrowQuant2.0 - maybe check that paths are pointing to the right places? I'm not too sure otherwise sorry. Hope that helps!

from marrowquant.

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